Red Rottweilers and “Unethical” Breeders

I am genuinely torn on the issue of dog breeders. On the one hand, I love dogs, and I have a fondness for particular dog breeds, and it’s the responsibility of breeders to produce more of those dogs so people like me can take a puppy home to treasure and train. Many breeders are lovely, responsible people even if they don’t know enough about population genetics to prevent inbreeding. While some breeders may view their studs as assembly lines, many do genuinely love their charges and take care to properly house and socialise their dogs and puppies.

I’ve put that disclaimer there. There it is. See that disclaimer? If you’re a dog breeder who loves your dogs, takes good care of their health and their need for companionship, and values the health of your dogs over their appearance, then you need not take the following rant personally in any way.

You might do so anyway, but as far as I’m concerned, I’ve covered my arse.

The adorable 9-month old rescue Rottweiler girl that we just adopted (blog post and pictures to follow) has slightly longer hair than Amos does, and it reminded me that there are long-haired Rottweilers in the world. Curious, I did a little research. It turns out that the long hair is a rare, recessive gene; it is not linked to any health issues.

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How cute is this guy? Photo from Molosserdogs.com

It is considered a “fault”. In show-breeding, that means the breed does not meet the standard. You really can’t show that dog, and most breeders will insist that if you take a long-haired rottie pup, you desex that dog when it comes of age so that it does not breed.

Let’s recap, because these concepts will return:

(a) long hair is part of the natural variation in the breed, i.e. it is not caused by outbreeding.

(b) long hair is not linked with poor health on the part of the animal.

(c)  For a recessive trait (like long hair) to express, you need two copies of the relevant allele, meaning one from each parent.

While apologists may argue that long hair is not necessarily very practical in a “working dog”, this can easily be rebutted by pointing out the numerous working dog breeds with long hair (oh, so many: border collies, long-haired german shepherds, mountain dogs, Old English sheepdogs…) and the fact that show dogs don’t tend to do a lot of work requiring a neat army buzz cut.

The production of long-haired rottweiler puppies means that both the parents have one copy of the long-haired allele. The breeder might decide not to repeat that cross, but they’re generally going to keep breeding those specific dogs to other dogs. This means that the carriers are still going to pass on that long-haired allele (50% chance per pup per parent with the allele).

This in turn means that not breeding the long-haired rotties does absolutely nothing to reduce the frequency of the allele in the population; it simply fails to increase it. As an attempt to remove genetic diversity from the population, it is both misguided and astonishingly ineffective. Even if it were effective, you would not only be removing that cosmetic change, but all the other genetic diversity linked to it, and purebred dogs can’t afford to lose any genetic diversity that doesn’t have a health cost.

So at this point I’m wondering why anyone – anyone – gives a crap if a rottie has long hair. They can still have the physique preferred for the dog. They’re still intelligent and loyal and strong. They still look like a rottie. Most importantly, they are healthy. It might be a bit tricker to comb for ticks and remove burrs, but otherwise, I’m drawing a blank. Maybe it makes it harder for judges to give points to a dog if there’s too much variation in the breed and they have to pick one variant over another.

I’m starting to take issue with the word “fault”.

The long-haired issue, however, is dwarfed by the issue of “red Rottweilers.”

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Another gorgeous one. Photo from the Rested Dog Inn at http://www.resteddoginn.ca/redrescue.php

These guys are fricking gorgeous, and they are, if anyone is curious, purebred rotties. Coat colour is a very complex polygenic trait. “Black with tan points”, the colour pattern one finds in rottweilers, is in itself the product of homozygous recessive genes that are fixed in the rottweiler population. All rotties have two copies of that allele.

In order to produce the “red” rottie (although I’d argue that’s more of a brown or liver colour), another gene needs to be altered. Once again, the alteration resulting in this colour is recessive and, much like the alleles for long hair, it’s quite rare in the population.

Again, the red coat is considered a fault. I curiously read more on this and came upon a rabid drool-flecked mouth-foaming rant on the subject by someone associated with the American Rottweiler Club, who used the phrase “corrupt the purity of our breed.”

They also stated that a breeder who sells a “red rottie” is to be considered “unethical,” because that dog can’t be shown and that such dogs should never, ever be bred. Furthermore, they said it was a sign of inbreeding.

Well… sort of. That’s hard to argue if you don’t know the incidence of the gene in the population. The best way to see if your dog is inbred as hell (other than assuming that purebreds are always inbred as hell, which is true to a point) is to look at the pedigree. If you can, go back more than the standard three to five generations. The only differences between a red or long-haired coat and a congenital internal recessive defect are that you can see the cosmetic changes and they’re not unhealthy. It is true that if you tried to breed for long hair or recessive coat colour, you would eventually create a highly inbred line. As the occasional result of a mating, it’s not a problem.

Then they tried to argue that this coat pigmentation is linked to problems in cardiac, eye and skin health.

“Gosh,” I thought to myself, “that sounds dire.”

Given that I still possess access to the university library, I signed onto Web of Science to do a little bit of a literature search for any studies showing a link between this particular pigmentation and any health problems.

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Curious.

Nothing.

Problems with white pigmentation have been heavily documented and researched elsewhere. A dog being brown instead of black… not so much. I tried every variation of keywords I could think of, and still…

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Zip. Nada. Nothing.

“Hrm,” I thought to myself, “that coat colouring looks familiar.”

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(Red and tan kelpie! photo from Noonbarra, kelpie breeders)

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A photo from a nice website on coat colour genetics in this breed. http://daminidachshunds.weebly.com/dachshund-color-genetics.html

“I wonder if it’s linked to health problems in those breeds? It’s clearly considered not a fault in those.”

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(look, I was getting tired of orthopteran insects, but the principle remains)

Now, in the interests of genetic honesty, it is possible that a particular condition might be linked to a health problem in one breed and not another, given how rapidly genes become fixed in these very small populations. It is possible.

But it’s not damn likely.

That makes it recap time!

(a) The red coat is part of the natural variation in the breed, i.e. it is not caused by outbreeding.

(b) The red hair is not linked with poor health on the part of the animal, and any attempts to state otherwise are clearly apologetics based on zero goddamn evidence and very likely confirmation bias (cf. confirmation bias: “This particular red rottweiler has a skin condition! I knew they were unhealthy!”).

(c)  For a recessive trait (like the red coat) to express, you need two copies of the relevant allele, meaning one from each parent.

The closest possibility is that the red coat appears to be strongly associated with lighter-coloured eyes, which are a bit more sensitive to sunlight. I have blue eyes. I relate. It’s really not something that affects my life in any major way.

In the cases of long hair and red coat, which are purely cosmetic differences as far as the dog is concerned and do not affect the strength, health, or conformation* of the animal, it is not possible to remove that diversity from the population without a genetic test to see if a parent dog carries the gene (except to, perhaps, make a note of it when these bundles of joy do turn up).

Labelling a breeder “unethical” for selling a perfectly healthy fucking dog?

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Trying to remove an allele from the population without having the faintest idea how to do it?

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Referring to the presence of a slightly different coat colour as a corruption as though it was best cast into the fires of Mount Doom? (“One phenotype to rule them all…”)

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This does not make sense. Breed standards exist for a reason, but they have gone well beyond that at this stage. I think it’s exceptionally telling that kelpie breeders in the U.S. refuse to allow their breed to be registered because they are concerned that their breed will be destroyed by show breeding. That is an entirely fair concern. I think it’s telling that the U.K. German Shepherd breed standards have been altered to consider that horrific sloping back a fault rather than a desirable trait.

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You have got to be fucking kidding me.

 

 

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See? That looks sensible. Photo taken from http://thegermanshepherddogbreed.blogspot.com.au/

Apparently it’s controversial.

Emphasising the health of the animal should never be controversial.

People who are selling red rotties and long-haired rotties as “rare rotties” might be accused of taking advantage of a genetic quirk and promoting aesthetics over temperament (although it’s a bit late to worry about that latter point), but they are hardly unethical. The only way it could be unethical would be if the breeder did not tell the buyer that the dog can’t be shown. Since I tend to consider dog shows somewhat in the light of obsessive public masturbation, this wouldn’t bother me (yes, yes, that’s just my opinion).

So if you see a long-haired or red rottie pup for sale and you melt into a pile of dog-adoring goo, be dissauded perhaps by the enormous responsibility of owning a large dog, or a dog at all; by the huge amount of work they are; by the possible vet bills you may be signing up for; but don’t, even for a second, be dissuaded by the mouth-breathing rants of breed purists.

*(don’t get me started on conformation; it’s like the word “holistic” – it has an actual, useful meaning, but mostly people who use it don’t mean it that way at all)

—-
P.S. When we got Amos as a puppy, I used to spend some time reading and researching things on a rottie enthusiast forum in a search for behavioural tips, until we found our current trainers. I’ve since stopped reading this forum because I am so tired of people talking about “For the BREED!” without actually meaning anything when they say this.

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Why I love the gym since this often confuses people… (Hypermobility, episode 1)

My love of the gym is weird to many. Here is my explanation (no, it’s not just endorphins)

When I was a kid, it didn’t take me too long to work out that most of the other kids were a bit different from me. It wasn’t the reading or the red hair or the good marks that really set me apart, at least not as far as I was concerned. It was the fact that other kids appeared to be able to do magical, superhero things with their bodies.

My first ever P.E. report (tender age of five) read, “Kate is unco-ordinated.” This meant nothing to me at the time. Looking back, it’s just a concise summary of how I felt.

I felt like, when all the other kids were receiving normal human kid-bodies that leapt and ran like fleet-footed bipedal gazelles and tumbled and swung like unusually tall spider monkeys, I had somehow been given a weird, lumpy, alien flesh-machine. Where others raced and flew, I bounced and flopped. I was out of breath. I was chubby. I couldn’t cross the monkey bars. Nothing seemed to quite work the way it should. There was nothing in particular wrong with me (this is true. I have always been able-bodied and am in no way trying to claim a disability here. This is just the story of how I live in my body). It all just felt wrong.

This didn’t stop me doing some things. I rode my bike (slowly). I swam (badly). I jumped rope (differently from how other people do it, which is relevant to this story – I never actually jumped, I just kind of stepped quickly and kicked my legs back). I liked stretching and doing forward somersaults on the big gym mats. These were my limits, though.

Some of the lack of co-ordination was down to undiagnosed short-sightedness. After I got laser eye surgery a few years back, it turns out that I can (at least sometimes) catch things thrown to me, rather than simply squeaking, ducking and trying to blindly bat them away from my head. That helped.

I felt like I could never quite explain why some things were so hard. I knew I was unfit, but that wasn’t the whole story. Things hurt. Joints hurt. Not in an arthritic way, not in a broken-bone way, and not in a “your muscles are just weak and will get stronger as you go” way.

Several years ago, I was having knee problems. My doctor explained that my patella was, and I quote: “rather like the surface of the moon.” Great. I’d started going to gym and doing high impact exercise, and this is what my freaking body does to me; it breaks its goddamn knees. Nice work, cartilage. Thanks a bunch.

A few years later, in the hope of running without knee pain, I started running barefoot, and discovered that I quite enjoyed it, but ultimately this lead to other problems.

Enter the physio and the podiatrist, and my current epiphany, which explains everything right down to why I never jumped rope the same way the other kids did.

The flailing. The bouncing. The hurting. The lack of control and co-ordination. It all comes down to range of motion. Since my joints are too mobile, I can’t control where they go – or rather, I can, but only if I am doing things very slowly and concentrating rather fiercely. This explains why I can’t run (at present) but why I can, in fact, swim without too much trouble (the water pressure contains the excess motion and it’s easier for me to be in charge of where all my limbs go). Swimming is glorious because it is, for me, almost pure cardio – the muscles work and build but they are not frantically working to keep my hips and ankles and knees where they should be. I’ll concede that it does get a bit trickier with a tank, 10+kgs of dive weights, and a current, and that there’s a reason I went with split fins for scuba diving.

My friend Nadia convinced me to try gym classes and I finally plucked up the courage to walk into a BodyPump class (this is back before the your-knee-is-full-of-craters conversation). If it sounds strange that one needs courage, most of my previous experiences of exercise with other people around tended to result in at least embarrassment on my part, if not downright humiliation.

I was a convert.

People look at me strangely for treating a trip to the gym as a reward for a job well done, and that’s fine. Not everyone likes gym. Weight training is gym training, essentially, and I will always love gym because of weight training (also stretching, but that’s another story).

When I train with weights, I am isolating muscle groups. I am working on one thing at a time. I am planting my feet or seated on a machine and I only have to worry about one set of joints. Usually the exercise is done in such a way that it braces joints anyway, although bench press gives me trouble because of my wrists (they don’t hurt, I’m just constantly rotating them to make sure they don’t tip back too far, because they really want to). Tricep kickbacks. Bicep curls.

One thing at a goddamn time, and it actually works and I can actually feel it. It feels right. It feels how I imagine most other people’s bodies feel most of the time. It doesn’t bounce and flop and hurt.

I can control my range of motion when I do weight training.

When I do other things that move too fast – aerobics classes, for example – I have to keep too many things in line at once. The hips will shift or the knees or the ankles or the wrists – something will go. While I am trying to keep those where they are supposed to be, that will overload the supporting muscles, so meanwhile the other muscles will try to compensate and get overloaded themselves, and it becomes a vortex of hypermobile disaster. I can do combat classes and step classes and so on, but I do them in a slow, low impact style because otherwise I’ll probably do my ankle.

The feeling of being in charge of how my body is moving has been so foreign to me, so unachievable, that doing a set of weights feels like I’m triumphantly flipping off the universe. I’m not amazing at weights. My technique is not perfect. All the same, when I do a clean-and-press, I might as well be dancing Swan Lake for how good I feel.

Learning how to run barefoot was like that, but multipled by hundreds, thousands, because I could never ever ever run before that. Running barefoot gave me more control over how my feet landed. Running in shoes makes me feel like I have weights glued to the end of my ankles. Remember how my ankles are hypermobile, and it’s hard enough to control where they go? Adding stiff, unbending weights to them multiplies the problem.

But running barefoot, unfortunately, means that, even though I am finally in charge of my feet to a marvellous and empowering degree, I am less in charge of my legs (at least, the right leg, which is the really stupid one). Not being in charge of my legs means I end up overloading my feet anyway (but at least not my knees. For once) (note: when I was starting out very slowly and working up to 5k barefoot, my legs actually survived the experience very well – but I did have to concentrate fiercely to keep my right leg landing straight on. Recently I started running again after a break and overdid it and now I have zero power to keep my leg straight).

At the moment the compromise is to have a very light, flexible shoe with orthotics in it. In combination with my physio strengthening exercises, it’s actually working quite well – the other day I completely forgot to change to my light shoes for the treadmill work and managed a good run without even noticing (very slight shin pain, so I’ve taken a few days off from running and will get back to it tomorrow).

In recent times I’ve investigated hypermobility more closely. It very much appears that I may have Ehlers-Danlo Syndrome / Hyper mobility type (or hypermobility syndrome, or joint hypermobility – names and classifications vary). I have the stretchy skin, the myopia (at least prior to the laser eye surgery), the sensitisation, the painful gut involvement, the (juvenile) asthma, the poor proprioception (exacerbated in the presence of progesterone. Yay?).

I also score 7/9 on the Beighton test – the only thing I can’t do is bend my thumbs back onto my arms, and apparently if you score 4 or more that fulfills a major criteria. The minor criteria include dislocations and subluxations (hell yes), myopia (yes), stretchy skin (yes, although I only worked this out recently when I realised that not everyone can pinch the skin on the back of their hand that way) and a bunch of other things.

In terms of classic hypermobility, it all does explain why I can’t do shoulder presses (my ligaments hurt) and even when I do the shoulders never get stronger, why I developed RSI from pipetting (Gilson pipettes – heavy spring action; I’m fine with Eppendorf and more lightweight and ergonomic pipettes) when no-one else seems to do so, and why stretching feels so amazing at the time and later on starts to hurt in a suspicious and sneaky way. It explains why I fell over at least once every day in primary school, why I could never cross the monkey bars, why it took me two years to learn to ride my bike without training wheels, why I can’t do cartwheels but I can put my hands flat on the ground without bending my legs, why I walk funny

I’ll be writing more on this as I am currently fascinated and it falls into my category of biomedical obsessions (with an intriguing genetic slant). The down side is that, since it is genetic, there’s no cure or treatment (so I’m stuck with the occasional agonising gut cramps that make me pass out but hey, codeine still works). The up side is that, if I know what’s going on, I have a much better chance of avoiding injury. I’ve already worked out some alternative weight training that will build muscles without overextending around the joint (i.e., no more shoulder presses or tricep presses. Assisted chin-ups and tricep pull-overs or kickbacks are much better).

I will also be visiting the local clinical pilates business and seeing if they can help me. Watch this space.

[This was originally posted on my private blog a few months ago, and the last few paragraphs were added in response to some reading I’ve been doing over the last few days. I feel as though I may have opened a biomechanical can of worms, here. – KN]

Animal breeding, genetics abuse, and Powerpoint pedigrees

I’m about to tell a little story, here, and be aware that there are far worse and far more egregious cases of what I’m going to call “genetics abuse” than the situation I am about to describe.

After dog training the other day, as we were walking Amos (our purebred Rottweiler, for those who don’t know) back to our car, a woman stepped out of our car and went “Oh, he’s beautiful!” (thank you, we know our dog is gorgeous).

“What line is he from?”

This question, well-intentioned as it is, makes me twitch. While we did glance at Amos’s pedigree (in my case, and as I’ll explain below, it was to calculate his inbreeding coefficient) and look at his parents’ records for eye examinations and elbow and hip scores, we don’t care what line he is from. We’re not breeders. We won’t breed Amos for a number of reasons. We got Amos from Oscelly because his parents were healthy and good-natured, and the breeders were supportive.

“Oscelly,” Husband replied politely. “In Kyneton.”

“I used to breed Rottweilers, in Queensland,” the woman explained. “But I can’t have another one since my last one died.”

I flooded with sympathy. “Oh, that’s awful,” I said.

“Yes, and there was no sign! I line-bred him as close as I could-”

At this point the conflict between “It’s so sad to lose a dog” and “you fucking idiot” caused a blood vessel to pop somewhere in the tact-zone of my brain. I actually inhaled my own spit when I went, “Ah… ha?”

“-and I’d been wrestling with him the night before, and he was fine, and I went out to the garage in the morning and he was dead. He was only seven.”

A healthy Rottweiler has a good chance of making it to ten years old and beyond. Quietly I observed, “Sounds like a heart problem?”

“Yes, I thought so.”

Then she admired Amos some more while he wriggled in sociable happiness, particularly his beautifully shaped head (he does have a nice head), and we parted ways. As in all truly frustrating situations, it actually took a few hours for me to get angry enough to start composing this post in my head.

Let Auntie Kate explain line-breeding to you, as well as some basic genetics, and let’s get cracking on what happened to this poor dog and his owner.

Line breeding is where a particular breeder/stud decides that they want their dogs (or horses, or cats, or alpacas) to have a particular look and tendency. They basically want a genetic stamp that says “These are our dogs. You have a dog from Stud X!” They also want all the traits that will allow them to win more dog shows, which will get them more stud fees. In order to achieve that, they try to concentrate the particular desired traits in their dogs.

They do this by inbreeding. Let’s be clear here: line breeding is just another way of saying “inbreeding.” There is no fucking around. It is the same thing, and it is very, very bad for any population to have this happen.

I know a good deal about population genetics (the thesis is coming along nicely) and next to nothing about animal husbandry. All that I know about animal husbandry is based on breeders of any kind of animal delivering bone-headed pronouncements that make me want to smack them upside the head with a population genetics text book (heavy enough to concuss). Having said that, animal husbandry is one of the long arms of human agriculture. Humanity has been breeding animals to conform to their specifications for millennia, and we’ve become pretty good at it. Without an understanding of DNA, or complex inheritance patterns, we managed to work out that breeding too close was a bad idea.

We worked this out from a number of signs: deformed offspring is one obvious sign. Less obvious signs are infertility or reduced fertility. If, for example, you want to buy a puppy from a breeder, and they announce that the bitch only had one pup in that litter, do not buy that pup. That pup has a good chance of breaking your heart. If you do cave, and buy the pup that almost certainly carries a number of recessive defects, do not breed the pup. Ever. If you do, you’re part of the problem.

So some animal husbandry has limits as to how close they are willing to breed their animals. They draw these limits far, far closer than they should, and then cite some pretty random research to say that this is okay. This research does not say what they think it says, and I’m going to explain why.

In every cell of your body*, you have two copies of your master genome** – the 23 (usually) chromosomes that are tightly wound strings of DNA. You have one copy from your biological mother, and one from your biological father. In the simplest scenario, when you produce gametes (eggs and sperm), each gamete contains only one copy. They might have your paternal copy, or your maternal copy (they might have a slight mix of the two as your chromosomes cross over and recombine, which is how new combinations arise). The successful gamete will pass that copy on to the next generation. Odds of having a mostly paternal versus a mostly maternal copy are 50:50.

So we have two copies of every gene and every gene region. When these copies are different in any way, we refer to the different versions as “alleles”. For example, I have red hair. Red hair is what we call a recessive trait, which means that I have to have inherited alleles relating to red hair from both my mother and my father (hair colour is actually a polygenic trait, so it’s not that simple, but both parents have to be involved for my hair colour to express the way it does). This also means that, since I have two copies of the relevant alleles, I am guaranteed to pass on one redhead allele copy to any kidlets I one day have.

So we’ve got the background for simple recessive inheritance. Now we get to the scary part.

YOU ARE A FILTHY MUTANT.

No, really, you are. DNA is self-replicating, and it even has proofreading systems to make sure it copies everything perfectly. It still screws up, and leads to mutations. We all have these mutations, every single one of us. Most of them are probably relatively benign on their own – after all, you’re reading this, right? – but in many cases if you had two copies, the result would be lethal. In fact, most of the time, if you have two copies that were flawed in the same way, you wouldn’t develop all the way to viability. You would be miscarried, maybe as a zygote, or an embryo, or a fetus.

Here’s the thing: because these mutations are so sparsely distributed throughout the genome, and so individual, and because there is so much diversity in the human genome (we have what is called a large effective population size, more on that later), it’s astoundingly rare that you will get two copies of a flawed allele (with the exception of some named recessive disorders that have persisted in the population – and there are some nasty ones out there).

Of course, if you’re closely related to someone, it’s much more likely that you both have that allele. I am now going to illustrate why cousins shouldn’t marry and have kids****, only in my example, they are DOG cousins.

(****early footnote to prevent offense also pasted in here: Of course, cousins are perfectly allowed to marry. It’s their right and their choice. It’s just that most of them seek genetic counselling to make sure that they are not going to pass on some deleterious recessive trait. In most cases, it’s perfectly fine.)

We begin with a basic pedigree.

Slide1

Meet Lord Doggington and Princess Jemima. They are both perfectly healthy, show line dogs of the breed I just made up called Zimbabwean Slothhounds. They win awards for how amazingly pretty they look. Depending on the breeder, they may also be valued for their robust strength and good nature, or the breeder might just be interested in appearance. Let’s give them the benefit of the doubt: they are, after all, particularly good at chasing down sloths.

Like all dogs – and all DNA-bearing organisms – Lord Doggington is carrying a nasty secret in his genome. It’s okay, because it arose with him due to a point mutation in one of his parents’ gametes, so it doesn’t exist anywhere else in the Zimbabwean Slothhound population. We should be safe from anyone ending up with two copies of this allele.

Alas, Lord Doggington’s owners think he is super awesome, and they want their whole stud to be like him. They want to concentrate his traits.

Lord Doggington and Lady Jemima have a bunch of puppies (ideally around eight). The stud sells six, and keeps two, Daisy and Fido, whom they like the look of. Daisy and Fido each have a 50% chance of inheriting Lord Doggington’s crap-arse allele. However, they will only ever have one copy, because Princess Jemima does not have the crap-arse allele. She probably has her own deleterious alleles, but we’ll focus on the other one here.

Slide2

Let’s imagine that both Daisy and Fido inherit the crap-arse allele. There is a 25% chance that this will happen (0.5 x 0.5 = 0.25, for those who forgot probability as soon as they graduated high school). Daisy and Fido are each bred to outstanding Slothhounds from other studs, and produce, respectively, Butcho and Miss Dogface, who are adorable puppies.

Slide3

There is a further 50% chance each that Miss Dogface and Butcho respectively will inherit the crap-arse allele from Fido and Daisy. If we know that Fido and Daisy have each inherited the allele, then, again, there is a 25% chance that both Miss Dogface and Butcho will as well. If we don’t know the status of Fido and Daisy – i.e., we’re just guessing, which is the fun part of recessive trait pedigrees – then there is a 25% chance that each pup will have the allele, and a 6.25% chance that both of them will. That’s a more than 1 in 20 chance; it’s actually quite high.

Let’s say that this untoward event happens, and the breeders decide to breed Dogface to Butcho (some breeders won’t do this. Some will. It varies) to create the pure strain of awesome that descended from Lord Doggington, thus elevating the Zimbabwean Slothhound from relative obscurity as a breed to glorious renown.

If we know that Dogface and Butcho have the crap-arse allele, there’s a 50% chance that their pup will have one copy, a 25% chance that they will have no copies, and a whopping remaining 25% chance the pup will have two copies. If it is still unknown – if, in fact, all we know is that Lord Doggington is on both sides of the pedigree and that Butcho and Dogface are first cousins – then we have a 1.56% chance that their offspring will have two copies of any allele from Lord Doggington. This is what we call the probability of identity by descent (IBD).*****

Slide4

In this last figure, I’ve now changed the colour to indicate that this unlikely event has happened, and we can see the carriers of the allele. The offspring of Miss Dogface and Butcho inherits both copies (something that is a 1.56% chance from the word go), and either aborts, or is born with a severe defect that may even require euthanasia. This is why you want to avoid dogs with tiny litter sizes – unless they’ve been bred for reduced ovulation, small litter sizes generally represent resorbed pups that did not develop or even useless gametes.

Lest you think 1.56% is vanishingly small, in a population-level analysis, it is huge. It is a matter of some concern, and this shit happens all the time. In livestock animals, offspring may often be bred back to their parents – now that you’ve got the basics, I’ll leave you to draw out the pedigree of all the shit that comes out of that.

When Amos’s breeder showed me his pedigree, he brought out a photo of his very own Lord Doggington, explained how fantastic that dog was, and that he was on both sides of Amos’s pedigree. This was stated to me as a good thing, and if I were not a geneticist, I would have been convinced by his superior knowledge. That is why I am writing this post and using too much bold typeface.

I gently pointed out that I was a population geneticist doing a PhD and that this was of some concern to me. The breeder told me about some research some fellow in the UK had done on plants where he experimented and showed that inbreeding wasn’t so bad.

I haven’t managed to find whatever research he was quoting, but here’s the question I want to ask: what sort of plant? Was it a native population? Because this, I think, is where animal husbandry and population geneticists part ways. Animal breeders know what I’ve just been explaining. These are not stupid people – they have a science all of their own. They’re just not updating it, and they are missing a crucial piece of the puzzle: the piece that comes from population genetics.

They are missing effective population size.

Effective population size is basically a way of describing the background genetic diversity in the population and what is passed on to the next generation. For example, you might have an enormous population of corals on a reef, but if the millions are all reproducing by cloning themselves, and if they are all descended from the same clone, the corals will have a very, very small population size (i.e.: 1). However, since they are clonal, they already have their two genome copies, and we already know that they are functional. There are advantages to clonality.

You might have a very large herd of deer, but if all the young males keep getting their arses handed to them by the boss male, he’s going to do all the mating. Because you have a large number of different females, the effective population size will be larger than 1, but it’s not going to be enormous. There’s going to be a lot of deer wandering around with that paternal genome copy.

The basic message is this: when you breed to concentrate physical traits in a population, you are removing variation from the genome, because you are not breeding the animals that don’t fit your requirements. These animals do not contribute to the next generation; therefore they are not included in your effective population size. You are concentrating the physical traits you desire, but you are also concentrating the invisible, deleterious alleles. You are increasing the likelihood that matings will result in double copies of the same rare, lethal allele. You are reducing your effective population size.

You are drying up your gene pool #nerdpun.

So inbreeding is tolerable and manageable when you have a large effective population size, although it is itself reducing your population diversity. It is a horrible thing to do when you have a small effective population size.

This just in: purebred dogs have a very small effective population size. We’re not talking clonal corals, but we’re definitely not talking human-grade levels either. It’s a closed system; generally they only breed purebreds of a breed to others. That’s the whole point. I decided to get a purebred dog despite knowing all this, because I grew up with and love the breed, and also because this way there is a measure of predictability regarding temperament (I like large dogs. Temperament is important) and disease (I want to know what to look for).

I decided to look at Amos’s pedigree myself. All up, his probability of any allele being identical by descent was less than 0.06%. Since I’d been told that the odds of finding a breeder who does not practice line breeding are slim to none, I decided that was an acceptable risk. Amos has an undershot jaw, so it would be irresponsible to breed him (it’s not a huge deal for him personally), but otherwise he is perfectly healthy.

I think. I’m not sure, because here’s the rub: Rottweilers became very fashionable at some point in the 1980s. Before that, they were known for the elbow and hip problems, and possibly the minor eye issues – and that was it. These are also common to many breeds of dog.

When a dog breed becomes fashionable, you get a lot of what is termed “backyard breeding” – people either breeding out of ignorance (because they like puppies), or greed (because purebred dogs are worth squagloads) or both. This means people didn’t necessarily check that their dogs were healthy before they bred them.

Rottweilers are now known for heart problems. This is a new thing. I now have to worry about my dog’s heart, because even though he has a 0.06% chance of identity by descent, the odds of these crappy heart alleles floating around are much higher (there’s also cancer. Don’t get me started).

And this woman I met in the parking lot – to come back to the point after a long and circuitous journey – line-bred her dog as close as she could, and she did it because she honestly believed that it would produce a healthier dog. She believed this because all the dogs she bred were outwardly healthy, with no consideration for or knowledge of what was hanging around unexpressed in their DNA. This is the problem. Because they don’t consider effective population size, because they don’t consider recessive traits, and because they do not acknowledge how common these mutations are, they only breed from the appearance and behaviour of the animal, i.e., from the phenotype, not the genotype (this is not universal: a number of recessive traits are very well understood and bred for, but this doesn’t connect with effective population size).

It’s possible that if she outbred her dogs with other studs – and you could even do this and keep a dog purebred – the resulting pup wouldn’t have had a congenital heart defect.

It’s just possible she wouldn’t have gone out to the garage and found her best mate dead on the floor at seven years old.

So, even in purebreeding systems, you can outbreed. Do that. Avoid genetic abuse. Reduce animal suffering. Avoid getting your heart broken.

*Except red blood cells. They need extra room for hauling around oxygen, so they don’t have a nucleus.

** We’re not talking about the mitochondrial genome. While that is important in its own way, it is only maternally inherited, it doesn’t recombine, and because cellular respiration is so crucial and you only have one copy rather than two, deleterious mutations don’t tend to survive.***

***Having said that, there are rare cases of species or individuals where a mitochondrion may be bi-parentally inherited and/or undergo recombination, and there are rare human diseases that are caused by mitochondrial mutations.

****Of course, cousins are perfectly allowed to marry. It’s their right and their choice. It’s just that most of them seek genetic counselling to make sure that they are not going to pass on some deleterious recessive trait. In most cases, it’s perfectly fine.

*****IBD! Identity by descent! Not to be confused with Isolation By Distance, or any other number of concepts for which IBD is an acronym…

(Backdated entry: Originally put together November 2012)